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  <h3><a href="#">Table Of Contents</a></h3>
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<li><a class="reference internal" href="#">MDAnalysis documentation</a><ul>
<li><a class="reference internal" href="#citation">Citation</a></li>
<li><a class="reference internal" href="#contents">Contents</a><ul>
</ul>
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<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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  <div class="section" id="mdanalysis-documentation">
<h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentation" title="Permalink to this headline">¶</a></h1>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
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<tbody valign="top">
<tr class="field"><th class="field-name">Release:</th><td class="field-body">0.7.5-devel</td>
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<tr class="field"><th class="field-name">Date:</th><td class="field-body">October 05, 2011</td>
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<p><strong>MDAnalysis</strong> is an object-oriented python toolkit to analyze molecular
dynamics trajectories generated by <a class="reference external" href="http://www.charmm.org/">CHARMM</a>, <a class="reference external" href="http://www.gromacs.org/">Gromacs</a>, <a class="reference external" href="http://ambermd.org/">Amber</a>, <a class="reference external" href="http://www.ks.uiuc.edu/Research/namd/">NAMD</a>, or
<a class="reference external" href="http://lammps.sandia.gov/">LAMMPS</a>; it also reads other formats (e.g. <a class="reference external" href="http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html">PDB</a> files and <a class="reference external" href="http://openbabel.org/wiki/XYZ_%28format%29">XYZ format</a>
trajectories; see <a class="reference internal" href="documentation_pages/coordinates/init.html#id1"><em>Table of Supported coordinate formats</em></a> for the full list). It
can write most of these formats, too, together with atom selections for use in
<a class="reference external" href="http://www.gromacs.org/">Gromacs</a>, <a class="reference external" href="http://www.charmm.org/">CHARMM</a>, <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> and <a class="reference external" href="http://www.pymol.org/">PyMol</a> (see <a class="reference internal" href="documentation_pages/selections_modules.html#selection-exporters"><em>Selection exporters</em></a>).</p>
<p>It allows one to read molecular dynamics trajectories and access the
atomic coordinates through <a class="reference external" href="http://numpy.scipy.org">NumPy</a> arrays. This provides a flexible and
relatively fast framework for complex analysis tasks. Fairly complete
atom <a class="reference internal" href="documentation_pages/selections.html#selection-commands-label"><em>Selection Commands</em></a> are implemented. Trajectories can
also be manipulated (for instance, fit to a reference structure) and
written out in a range of formats.</p>
<p><strong>Source code</strong> is available from <a class="reference external" href="http://mdanalysis.googlecode.com">http://mdanalysis.googlecode.com</a> under the
<a class="reference external" href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GNU Public Licence, version 2</a>, together with some additional documentation.</p>
<p>Please report <strong>bugs</strong> or <strong>enhancement requests</strong> through the <a class="reference external" href="http://code.google.com/p/mdanalysis/issues/list">Issue
Tracker</a>. Questions can also be asked on the <a class="reference external" href="http://groups.google.com/group/mdnalysis-discussion">mdnalysis-discussion mailing
list</a>.</p>
<div class="section" id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this headline">¶</a></h2>
<p>When using MDAnalysis in published work, please cite</p>
<ul class="simple">
<li>N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
Dynamics Simulations. <em>J. Comput. Chem.</em> <strong>32</strong> (2011), 2319–2327.
doi:<a class="reference external" href="http://dx.doi.org/10.1002/jcc.21787">10.1002/jcc.21787</a></li>
</ul>
<p class="rubric">Included algorithms</p>
<p>If you use the RMSD alignment code (<a class="reference internal" href="documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align" title="MDAnalysis.analysis.align"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a>)
that uses the <a class="reference internal" href="documentation_pages/core/qcprot.html#module-MDAnalysis.core.qcprot" title="MDAnalysis.core.qcprot"><tt class="xref py py-mod docutils literal"><span class="pre">qcprot</span></tt></a> module please also cite</p>
<ul class="simple">
<li>Douglas L. Theobald. Rapid calculation of RMSD using a
quaternion-based characteristic polynomial. <em>Acta
Crystallographica A</em> <strong>61</strong> (2005), 478-480.</li>
<li>Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
determination of the optimal rotational matrix for macromolecular
superpositions. <em>J. Comput. Chem.</em> <strong>31</strong> (2010), 1561–1563.</li>
</ul>
<p>If you use the helix analysis algorithm <a class="reference external" href="http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html">HELANAL</a> in
<a class="reference internal" href="documentation_pages/analysis/helanal.html#module-MDAnalysis.analysis.helanal" title="MDAnalysis.analysis.helanal"><tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis.helanal</span></tt></a> please cite</p>
<ul class="simple">
<li>Bansal M, Kumar S, Velavan R. 2000. HELANAL — A program to characterise
helix geometry in proteins. <em>J. Biomol. Struct. Dyn.</em> <strong>17</strong>, 811–819</li>
</ul>
<p>Thanks!</p>
</div>
<div class="section" id="contents">
<h2>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/overview.html">1. Overview over MDAnalysis</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/selections.html">2. Selection Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/analysis_modules.html">3. Analysis modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/topology_modules.html">4. Topology modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/coordinates_modules.html">5. Coordinates modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/selections_modules.html">6. Selection exporters</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/core_modules.html">7. Core modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation_pages/KDTree_modules.html">8. KDTree module</a></li>
</ul>
</div>
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<div class="section" id="indices-and-tables">
<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
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